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Formation and Maintenance of Tissue Resident Memory CD8+ T Cells after Viral Infection.

Topham DJ, Reilly EC, Emo KL, Sportiello M.

Pathogens. 2019 Oct 18;8(4). pii: E196. doi: 10.3390/pathogens8040196. Review.


Comparison of human H3N2 antibody responses elicited by egg-based, cell-based, and recombinant protein-based influenza vaccines during the 2017-2018 season.

Gouma S, Zost SJ, Parkhouse K, Branche A, Topham DJ, Cobey S, Hensley SE.

Clin Infect Dis. 2019 Oct 9. pii: ciz996. doi: 10.1093/cid/ciz996. [Epub ahead of print]


Role of Memory B Cells in Hemagglutinin-Specific Antibody Production Following Human Influenza A Virus Infection.

Sangster MY, Nguyen PQT, Topham DJ.

Pathogens. 2019 Sep 28;8(4). pii: E167. doi: 10.3390/pathogens8040167. Review.


Microbiome-Transcriptome Interactions Related to Severity of Respiratory Syncytial Virus Infection.

Sonawane AR, Tian L, Chu CY, Qiu X, Wang L, Holden-Wiltse J, Grier A, Gill SR, Caserta MT, Falsey AR, Topham DJ, Walsh EE, Mariani TJ, Weiss ST, Silverman EK, Glass K, Liu YY.

Sci Rep. 2019 Sep 25;9(1):13824. doi: 10.1038/s41598-019-50217-w.


Interferon-Induced Protein 44 Interacts with Cellular FK506-Binding Protein 5, Negatively Regulates Host Antiviral Responses, and Supports Virus Replication.

DeDiego ML, Nogales A, Martinez-Sobrido L, Topham DJ.

MBio. 2019 Aug 27;10(4). pii: e01839-19. doi: 10.1128/mBio.01839-19.


Monoclonal Antibody Responses after Recombinant Hemagglutinin Vaccine versus Subunit Inactivated Influenza Virus Vaccine: a Comparative Study.

Henry C, Palm AE, Utset HA, Huang M, Ho IY, Zheng NY, Fitzgerald T, Neu KE, Chen YQ, Krammer F, Treanor JJ, Sant AJ, Topham DJ, Wilson PC.

J Virol. 2019 Oct 15;93(21). pii: e01150-19. doi: 10.1128/JVI.01150-19. Print 2019 Nov 1.


Novel Functions of IFI44L as a Feedback Regulator of Host Antiviral Responses.

DeDiego ML, Martinez-Sobrido L, Topham DJ.

J Virol. 2019 Oct 15;93(21). pii: e01159-19. doi: 10.1128/JVI.01159-19. Print 2019 Nov 1.


Programming of Distinct Chemokine-Dependent and -Independent Search Strategies for Th1 and Th2 Cells Optimizes Function at Inflamed Sites.

Gaylo-Moynihan A, Prizant H, Popović M, Fernandes NRJ, Anderson CS, Chiou KK, Bell H, Schrock DC, Schumacher J, Capece T, Walling BL, Topham DJ, Miller J, Smrcka AV, Kim M, Hughson A, Fowell DJ.

Immunity. 2019 Aug 20;51(2):298-309.e6. doi: 10.1016/j.immuni.2019.06.026. Epub 2019 Aug 6.


Measuring the Severity of Respiratory Illness in the First 2 Years of Life in Preterm and Term Infants.

Caserta MT, Yang H, Bandyopadhyay S, Qiu X, Gill SR, Java J, McDavid A, Falsey AR, Topham DJ, Holden-Wiltse J, Scheible K, Pryhuber G.

J Pediatr. 2019 Jul 31. pii: S0022-3476(19)30825-X. doi: 10.1016/j.jpeds.2019.06.061. [Epub ahead of print]


Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study.

Walsh EE, Mariani TJ, Chu C, Grier A, Gill SR, Qiu X, Wang L, Holden-Wiltse J, Corbett A, Thakar J, Benoodt L, McCall MN, Topham DJ, Falsey AR, Caserta MT.

JMIR Res Protoc. 2019 Jun 6;8(6):e12907. doi: 10.2196/12907.


Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure.

Zhang Y, Bandyopadhyay G, Topham DJ, Falsey AR, Qiu X.

BMC Bioinformatics. 2019 Apr 15;20(1):185. doi: 10.1186/s12859-019-2783-8.


Influenza Virus Vaccination Elicits Poorly Adapted B Cell Responses in Elderly Individuals.

Henry C, Zheng NY, Huang M, Cabanov A, Rojas KT, Kaur K, Andrews SF, Palm AE, Chen YQ, Li Y, Hoskova K, Utset HA, Vieira MC, Wrammert J, Ahmed R, Holden-Wiltse J, Topham DJ, Treanor JJ, Ertl HC, Schmader KE, Cobey S, Krammer F, Hensley SE, Greenberg H, He XS, Wilson PC.

Cell Host Microbe. 2019 Mar 13;25(3):357-366.e6. doi: 10.1016/j.chom.2019.01.002. Epub 2019 Feb 19.


Broad Hemagglutinin-Specific Memory B Cell Expansion by Seasonal Influenza Virus Infection Reflects Early-Life Imprinting and Adaptation to the Infecting Virus.

Tesini BL, Kanagaiah P, Wang J, Hahn M, Halliley JL, Chaves FA, Nguyen PQT, Nogales A, DeDiego ML, Anderson CS, Ellebedy AH, Strohmeier S, Krammer F, Yang H, Bandyopadhyay S, Ahmed R, Treanor JJ, Martinez-Sobrido L, Golding H, Khurana S, Zand MS, Topham DJ, Sangster MY.

J Virol. 2019 Apr 3;93(8). pii: e00169-19. doi: 10.1128/JVI.00169-19. Print 2019 Apr 15.


Modulation of Innate Immune Responses by the Influenza A NS1 and PA-X Proteins.

Nogales A, Martinez-Sobrido L, Topham DJ, DeDiego ML.

Viruses. 2018 Dec 12;10(12). pii: E708. doi: 10.3390/v10120708. Review.


Neonatal gut and respiratory microbiota: coordinated development through time and space.

Grier A, McDavid A, Wang B, Qiu X, Java J, Bandyopadhyay S, Yang H, Holden-Wiltse J, Kessler HA, Gill AL, Huyck H, Falsey AR, Topham DJ, Scheible KM, Caserta MT, Pryhuber GS, Gill SR.

Microbiome. 2018 Oct 26;6(1):193. doi: 10.1186/s40168-018-0566-5.


Directed selection of amino acid changes in the influenza hemagglutinin and neuraminidase affecting protein antigenicity.

DeDiego ML, Chiem K, Topham DJ.

Vaccine. 2018 Oct 15;36(43):6383-6392. doi: 10.1016/j.vaccine.2018.09.005. Epub 2018 Sep 14.


Functional Evolution of the 2009 Pandemic H1N1 Influenza Virus NS1 and PA in Humans.

Nogales A, Martinez-Sobrido L, Chiem K, Topham DJ, DeDiego ML.

J Virol. 2018 Sep 12;92(19). pii: e01206-18. doi: 10.1128/JVI.01206-18. Print 2018 Oct 1.


Crowd on a Chip: Label-Free Human Monoclonal Antibody Arrays for Serotyping Influenza.

Zhang H, Henry C, Anderson CS, Nogales A, DeDiego ML, Bucukovski J, Martinez-Sobrido L, Wilson PC, Topham DJ, Miller BL.

Anal Chem. 2018 Aug 7;90(15):9583-9590. doi: 10.1021/acs.analchem.8b02479. Epub 2018 Jul 20.


Pandemic influenza vaccines: what they have taught us about B cell immunology.

Topham DJ, Nguyen P, Sangster MY.

Curr Opin Immunol. 2018 Aug;53:203-208. doi: 10.1016/j.coi.2018.06.004. Epub 2018 Jun 26. Review.


T-Cell Responses in Adults During Natural Respiratory Syncytial Virus Infection.

Roumanes D, Falsey AR, Quataert S, Secor-Socha S, Lee FE, Yang H, Bandyopadhyay S, Holden-Wiltse J, Topham DJ, Walsh EE.

J Infect Dis. 2018 Jul 2;218(3):418-428. doi: 10.1093/infdis/jiy016.


Effect of prior vaccination on carriage rates of Streptococcus pneumoniae in older adults: A longitudinal surveillance study.

Branche AR, Yang H, Java J, Holden-Wiltse J, Topham DJ, Peasley M, Frost MR, Nahm MH, Falsey AR.

Vaccine. 2018 Jul 5;36(29):4304-4310. doi: 10.1016/j.vaccine.2018.05.107. Epub 2018 Jun 2.


CD4 T Cell Epitope Specificity and Cytokine Potential Are Preserved as Cells Transition from the Lung Vasculature to Lung Tissue following Influenza Virus Infection.

DiPiazza A, Laniewski N, Rattan A, Topham DJ, Miller J, Sant AJ.

J Virol. 2018 Jun 13;92(13). pii: e00377-18. doi: 10.1128/JVI.00377-18. Print 2018 Jul 1.


Broad cross-reactive IgG responses elicited by adjuvanted vaccination with recombinant influenza hemagglutinin (rHA) in ferrets and mice.

Wang J, Hilchey SP, DeDiego M, Perry S, Hyrien O, Nogales A, Garigen J, Amanat F, Huertas N, Krammer F, Martinez-Sobrido L, Topham DJ, Treanor JJ, Sangster MY, Zand MS.

PLoS One. 2018 Apr 11;13(4):e0193680. doi: 10.1371/journal.pone.0193680. eCollection 2018.


Tissue-Resident Memory CD8+ T Cells: From Phenotype to Function.

Topham DJ, Reilly EC.

Front Immunol. 2018 Mar 26;9:515. doi: 10.3389/fimmu.2018.00515. eCollection 2018. Review.


Influenza Infection in Humans Induces Broadly Cross-Reactive and Protective Neuraminidase-Reactive Antibodies.

Chen YQ, Wohlbold TJ, Zheng NY, Huang M, Huang Y, Neu KE, Lee J, Wan H, Rojas KT, Kirkpatrick E, Henry C, Palm AE, Stamper CT, Lan LY, Topham DJ, Treanor J, Wrammert J, Ahmed R, Eichelberger MC, Georgiou G, Krammer F, Wilson PC.

Cell. 2018 Apr 5;173(2):417-429.e10. doi: 10.1016/j.cell.2018.03.030.


Virus-Specific Antibody, Viral Load, and Disease Severity in Respiratory Syncytial Virus Infection.

Walsh EE, Wang L, Falsey AR, Qiu X, Corbett A, Holden-Wiltse J, Mariani TJ, Topham DJ, Caserta MT.

J Infect Dis. 2018 Jun 20;218(2):208-217. doi: 10.1093/infdis/jiy106.


Publisher Correction: Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain.

Anderson CS, Ortega S, Chaves FA, Clark AM, Yang H, Topham DJ, DeDiego ML.

Sci Rep. 2018 Mar 6;8(1):4265. doi: 10.1038/s41598-018-22372-z.


T cell developmental arrest in former premature infants increases risk of respiratory morbidity later in infancy.

Scheible KM, Emo J, Laniewski N, Baran AM, Peterson DR, Holden-Wiltse J, Bandyopadhyay S, Straw AG, Huyck H, Ashton JM, Tripi KS, Arul K, Werner E, Scalise T, Maffett D, Caserta M, Ryan RM, Reynolds AM, Ren CL, Topham DJ, Mariani TJ, Pryhuber GS.

JCI Insight. 2018 Feb 22;3(4). pii: 96724. doi: 10.1172/jci.insight.96724. eCollection 2018 Feb 22.


Antigenic cartography of H1N1 influenza viruses using sequence-based antigenic distance calculation.

Anderson CS, McCall PR, Stern HA, Yang H, Topham DJ.

BMC Bioinformatics. 2018 Feb 12;19(1):51. doi: 10.1186/s12859-018-2042-4.


Publisher Correction: Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain.

Anderson CS, Ortega S, Chaves FA, Clark AM, Yang H, Topham DJ, DeDiego ML.

Sci Rep. 2018 Jan 5;8(1):276. doi: 10.1038/s41598-017-17926-6.


Antigenicity of the 2015-2016 seasonal H1N1 human influenza virus HA and NA proteins.

Clark AM, DeDiego ML, Anderson CS, Wang J, Yang H, Nogales A, Martinez-Sobrido L, Zand MS, Sangster MY, Topham DJ.

PLoS One. 2017 Nov 16;12(11):e0188267. doi: 10.1371/journal.pone.0188267. eCollection 2017.


Natural and directed antigenic drift of the H1 influenza virus hemagglutinin stalk domain.

Anderson CS, Ortega S, Chaves FA, Clark AM, Yang H, Topham DJ, DeDiego ML.

Sci Rep. 2017 Nov 6;7(1):14614. doi: 10.1038/s41598-017-14931-7. Erratum in: Sci Rep. 2018 Jan 5;8(1):276. Sci Rep. 2018 Mar 6;8(1):4265.


Association of Dynamic Changes in the CD4 T-Cell Transcriptome With Disease Severity During Primary Respiratory Syncytial Virus Infection in Young Infants.

Mariani TJ, Qiu X, Chu C, Wang L, Thakar J, Holden-Wiltse J, Corbett A, Topham DJ, Falsey AR, Caserta MT, Walsh EE.

J Infect Dis. 2017 Nov 15;216(8):1027-1037. doi: 10.1093/infdis/jix400.


A novel intracellular pool of LFA-1 is critical for asymmetric CD8+ T cell activation and differentiation.

Capece T, Walling BL, Lim K, Kim KD, Bae S, Chung HL, Topham DJ, Kim M.

J Cell Biol. 2017 Nov 6;216(11):3817-3829. doi: 10.1083/jcb.201609072. Epub 2017 Sep 27.


The K186E Amino Acid Substitution in the Canine Influenza Virus H3N8 NS1 Protein Restores Its Ability To Inhibit Host Gene Expression.

Nogales A, Chauché C, DeDiego ML, Topham DJ, Parrish CR, Murcia PR, Martínez-Sobrido L.

J Virol. 2017 Oct 27;91(22). pii: e00877-17. doi: 10.1128/JVI.00877-17. Print 2017 Nov 15.


Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness.

Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR.

Sci Rep. 2017 Jul 26;7(1):6548. doi: 10.1038/s41598-017-06738-3.


Functional Evolution of Influenza Virus NS1 Protein in Currently Circulating Human 2009 Pandemic H1N1 Viruses.

Clark AM, Nogales A, Martinez-Sobrido L, Topham DJ, DeDiego ML.

J Virol. 2017 Aug 10;91(17). pii: e00721-17. doi: 10.1128/JVI.00721-17. Print 2017 Sep 1.


Interplay of PA-X and NS1 Proteins in Replication and Pathogenesis of a Temperature-Sensitive 2009 Pandemic H1N1 Influenza A Virus.

Nogales A, Rodriguez L, DeDiego ML, Topham DJ, Martínez-Sobrido L.

J Virol. 2017 Aug 10;91(17). pii: e00720-17. doi: 10.1128/JVI.00720-17. Print 2017 Sep 1.


Maximum Likelihood Estimation of Titer via a Power Family of Four-Parameter Logistic Model.

Yang H, Holden-Wiltse J, Topham DJ, Treanor J.

J Biopharm Stat. 2018;28(3):492-500. doi: 10.1080/10543406.2017.1333996. Epub 2017 Sep 5.


FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis.

Zhang Y, Topham DJ, Thakar J, Qiu X.

Bioinformatics. 2017 Jul 1;33(13):1944-1952. doi: 10.1093/bioinformatics/btx104.


B-Cell Responses to Intramuscular Administration of a Bivalent Virus-Like Particle Human Norovirus Vaccine.

Ramani S, Neill FH, Ferreira J, Treanor JJ, Frey SE, Topham DJ, Goodwin RR, Borkowski A, Baehner F, Mendelman PM, Estes MK, Atmar RL.

Clin Vaccine Immunol. 2017 May 5;24(5). pii: e00571-16. doi: 10.1128/CVI.00571-16. Print 2017 May.


A live-attenuated influenza vaccine for H3N2 canine influenza virus.

Rodriguez L, Nogales A, Reilly EC, Topham DJ, Murcia PR, Parrish CR, Martinez Sobrido L.

Virology. 2017 Apr;504:96-106. doi: 10.1016/j.virol.2017.01.020. Epub 2017 Feb 3.


Development of a Global Respiratory Severity Score for Respiratory Syncytial Virus Infection in Infants.

Caserta MT, Qiu X, Tesini B, Wang L, Murphy A, Corbett A, Topham DJ, Falsey AR, Holden-Wiltse J, Walsh EE.

J Infect Dis. 2017 Mar 1;215(5):750-756. doi: 10.1093/infdis/jiw624. Erratum in: J Infect Dis. 2017 Sep 15;216(6):786.


NS1 Protein Amino Acid Changes D189N and V194I Affect Interferon Responses, Thermosensitivity, and Virulence of Circulating H3N2 Human Influenza A Viruses.

Nogales A, Martinez-Sobrido L, Topham DJ, DeDiego ML.

J Virol. 2017 Feb 14;91(5). pii: e01930-16. doi: 10.1128/JVI.01930-16. Print 2017 Mar 1.


Temperature-Sensitive Live-Attenuated Canine Influenza Virus H3N8 Vaccine.

Nogales A, Rodriguez L, Chauché C, Huang K, Reilly EC, Topham DJ, Murcia PR, Parrish CR, Martínez-Sobrido L.

J Virol. 2017 Jan 31;91(4). pii: e02211-16. doi: 10.1128/JVI.02211-16. Print 2017 Feb 15.


The Effects of Acute Neutrophil Depletion on Resolution of Acute Influenza Infection, Establishment of Tissue Resident Memory (TRM), and Heterosubtypic Immunity.

Reilly EC, Lambert-Emo K, Topham DJ.

PLoS One. 2016 Oct 14;11(10):e0164247. doi: 10.1371/journal.pone.0164247. eCollection 2016.


Live Imaging of Influenza Infection of the Trachea Reveals Dynamic Regulation of CD8+ T Cell Motility by Antigen.

Lambert Emo K, Hyun YM, Reilly E, Barilla C, Gerber S, Fowell D, Kim M, Topham DJ.

PLoS Pathog. 2016 Sep 19;12(9):e1005881. doi: 10.1371/journal.ppat.1005881. eCollection 2016 Sep.


NS1 Protein Mutation I64T Affects Interferon Responses and Virulence of Circulating H3N2 Human Influenza A Viruses.

DeDiego ML, Nogales A, Lambert-Emo K, Martinez-Sobrido L, Topham DJ.

J Virol. 2016 Oct 14;90(21):9693-9711. doi: 10.1128/JVI.01039-16. Print 2016 Nov 1.


Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates.

Anderson CS, DeDiego ML, Thakar J, Topham DJ.

PLoS One. 2016 Aug 5;11(8):e0160510. doi: 10.1371/journal.pone.0160510. eCollection 2016.


Both Neutralizing and Non-Neutralizing Human H7N9 Influenza Vaccine-Induced Monoclonal Antibodies Confer Protection.

Henry Dunand CJ, Leon PE, Huang M, Choi A, Chromikova V, Ho IY, Tan GS, Cruz J, Hirsh A, Zheng NY, Mullarkey CE, Ennis FA, Terajima M, Treanor JJ, Topham DJ, Subbarao K, Palese P, Krammer F, Wilson PC.

Cell Host Microbe. 2016 Jun 8;19(6):800-13. doi: 10.1016/j.chom.2016.05.014.

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